Protein Info for LU632_RS12555 in Erwinia tracheiphila SCR3

Name: topA
Annotation: type I DNA topoisomerase

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 870 TIGR01051: DNA topoisomerase I" amino acids 5 to 634 (630 residues), 835 bits, see alignment E=2.9e-255 PF01751: Toprim" amino acids 5 to 142 (138 residues), 73.1 bits, see alignment E=4.4e-24 PF01131: Topoisom_bac" amino acids 157 to 564 (408 residues), 419.9 bits, see alignment E=3e-129 PF01396: zf-C4_Topoisom" amino acids 597 to 622 (26 residues), 24.8 bits, see alignment (E = 3.8e-09) amino acids 709 to 745 (37 residues), 43.1 bits, see alignment (E = 7.5e-15) amino acids 763 to 792 (30 residues), 8.6 bits, see alignment (E = 0.00045) PF21372: TOP1_ZnF" amino acids 651 to 695 (45 residues), 95.2 bits, see alignment 3.8e-31 PF08272: Topo_Zn_Ribbon" amino acids 758 to 793 (36 residues), 46 bits, see alignment (E = 8.6e-16) amino acids 824 to 863 (40 residues), 76.2 bits, see alignment 3e-25

Best Hits

Swiss-Prot: 85% identical to TOP1_ECOLI: DNA topoisomerase 1 (topA) from Escherichia coli (strain K12)

KEGG orthology group: K03168, DNA topoisomerase I [EC: 5.99.1.2] (inferred from 87% identity to eay:EAM_1870)

MetaCyc: 85% identical to DNA topoisomerase I (Escherichia coli K-12 substr. MG1655)
5.99.1.2-RXN [EC: 5.6.2.1]

Predicted SEED Role

"DNA topoisomerase I (EC 5.99.1.2)" in subsystem Conserved gene cluster associated with Met-tRNA formyltransferase or DNA topoisomerases, Type I, ATP-independent or pVir Plasmid of Campylobacter (EC 5.99.1.2)

Isozymes

Compare fitness of predicted isozymes for: 5.99.1.2

Use Curated BLAST to search for 5.6.2.1 or 5.99.1.2

Sequence Analysis Tools

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search structures

Predict protein localization: PSORTb (Gram-negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the current SEED with FIGfam search

Find homologs in fast.genomics or the ENIGMA genome browser

Find the best match in UniProt

Protein Sequence (870 amino acids)

>LU632_RS12555 type I DNA topoisomerase (Erwinia tracheiphila SCR3)
MGKALVIVESPAKAKTINKYLGNDYVVKSSVGHIRDLPTSGSTVKKSTDSTTSKTTKKVK
KDEKAALVSRMGVDPYNGWDANYQILPGKEKVVSELKALAENADHIYLATDLDREGEAIA
WHLREVIGGDDSRFSRVVFNEITKNAIRHAFDKPGELNISRVNAQQARRFMDRVVGYMVS
PLLWKKIARGLSAGRVQSVAVRLVVEREHEIKAFVPEEYWELHANLNTPRGNDLLMEVTH
HHDSPFKPVNSEQTQAAVSLLENALYRVAEREDKPTSSKPGAPFITSTLQQAASTRLGYG
VKKTMMMAQRLYEAGHITYMRTDSTNISQDALSMVRDYIDNAFGTQYLPKDPNVYASKDN
SQEAHEAIRPSDVDVLSEQLKDMEADAQKLYQLIWRQFVACQMVPAKYDATTLTVNAGDF
KLKARGRTLRFDGWTRVMPALRKGDEDRSLPLIEVGEALTLLQLKPSQHFTKPPARFSEA
SLVRELEKRGIGRPSTYASIISTIQDRGYVRVDSRRFYAEKMGEIVTNRLEENFRELMNY
DFTAHMENNLDLVANNEAQWKSVLDTFFTDFSQQLEKADKDPEEGGMQPNQMILTSIDCP
TCGRKMGIRTASTGVFLGCSGYALPPKERCKQTINLIPENEVLNVLEGEDAETNALRARR
RCGKCGTAMDSYLIDNQSKLHVCGNNPGCDGYEIEQGEFRIKGYDGPIVECEKCGSEMHL
KMGRFGKYMACINDECKNTRKILRNGDIAPPKEDPVPLPELACEKSDAHFVLRDGAAGVF
LAASTFPKSRETRAPLVEELLRFRERLPEKLRYLADAPVADDQGNKTVVRYSRKTKQQYV
STDKDGKATGWSAFYVDGKWQITSKTAAKK